HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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TGP
1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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SGDP
Simons Genome Diversity Project
Populations: 130
Individuals: 278
Ancestry analyses:6,800,992
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Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

rs565518333
Alleles:
reference
T
ancestral
alternate
A
derived
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
How was the ancestral/derived state determined?Chromosome 10   position  31,785,767  (GRCh37) Explore rs565518333 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 96.3%
3.7%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
SAS 100.0%
0.0%
WEA 100.0%
0.0%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Joint clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP385.7 generations 99  =  1  +  981.000
Pairwise results table Joint clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Tubalar-1B + S_Mansi-2B Concordant SGDP 31,374,847 – 31,983,119 608,271.5 0.45444956 8 656.5300 243.7
S_Tubalar-1B + B_French-3B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 11 138.2450 1,591.4
S_Tubalar-1B + S_Jordanian-2B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Iraqi_Jew-1A Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Mansi-2B + S_Spanish-1A Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 7 50.0281 2,798.4
S_Mansi-2B + S_Icelandic-1B Discordant SGDP 31,687,839 – 32,277,373 589,533.5 0.43464838 70 631.6948 2,216.3
S_Mansi-2B + S_Kalash-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Papuan-10B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Ulchi-1B Discordant SGDP 31,112,961 – 31,795,978 683,016.5 0.28118483 33 553.7958 1,191.8
S_Tubalar-1B + S_Ulchi-2B Discordant SGDP 31,134,695 – 31,795,978 661,282.5 0.24516534 40 514.5479 1,554.8
S_Tubalar-1B + S_Altaian-1B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Tubalar-2A Discordant SGDP 31,040,456 – 31,785,796 745,340.5 0.37033092 48 655.0282 1,465.6
S_Tubalar-1B + S_Quechua-1A Discordant SGDP 31,134,695 – 31,785,796 651,101.0 0.24402329 52 508.7471 2,044.2
S_Tubalar-1B + S_Zapotec-2A Discordant SGDP 31,112,961 – 31,785,796 672,835.0 0.28004278 47 547.9950 1,715.3
S_Tubalar-1B + S_Piapoco-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Maori-1A Discordant SGDP 31,565,428 – 31,785,796 220,368.0 0.00715912 10 112.5039 1,777.7
S_Tubalar-1B + S_Even-3A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Papuan-12B Discordant SGDP 31,565,428 – 32,048,924 483,495.5 0.34492814 18 509.0204 707.2
S_Tubalar-1B + S_Yakut-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Georgian-2B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Naxi-3B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Orcadian-1B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Miao-1B Discordant SGDP 31,068,515 – 31,785,796 717,281.5 0.33399940 42 612.4946 1,371.4
S_Tubalar-1B + S_Mixtec-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Dai-3B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Bergamo-2B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Han-1B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Orcadian-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Tu-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Chane-1A Discordant SGDP 31,134,695 – 31,785,796 651,101.0 0.24402329 52 508.7471 2,044.2
S_Tubalar-1B + S_Uygur-1A Discordant SGDP 31,040,456 – 31,795,978 755,522.0 0.37147296 50 660.8289 1,513.3
S_Mansi-2B + S_Mozabite-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Yi-2B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Mansi-2B + S_Papuan-1B Discordant SGDP 31,583,614 – 32,048,924 465,309.5 0.34332781 19 499.0108 761.5
S_Tubalar-1B + S_She-2A Discordant SGDP 31,041,075 – 31,795,978 754,902.5 0.36680613 60 656.7981 1,827.0
S_Mansi-2B + S_Papuan-7B Discordant SGDP 31,583,614 – 32,048,924 465,309.5 0.34332781 19 499.0108 761.5
S_Tubalar-1B + S_Tu-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Brahmin-1B Discordant SGDP 31,785,735 – 33,267,537 1,481,802.0 0.80756294 139 1,358.3153 2,046.7
S_Tubalar-1B + S_Korean-2B Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 7 50.0281 2,798.4
S_Mansi-2B + S_French-1A Discordant SGDP 31,565,428 – 31,785,796 220,368.0 0.00715912 10 112.5039 1,777.7
S_Tubalar-1B + S_Burmese-1B Discordant SGDP 31,040,456 – 31,795,978 755,522.0 0.37147296 52 660.8289 1,573.8
S_Mansi-2B + S_Greek-1A Discordant SGDP 31,144,556 – 31,868,351 723,795.0 0.24543891 39 544.7727 1,431.8
S_Tubalar-1B + S_Thai-1A Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Mansi-2B + S_Tuscan-2B Discordant SGDP 31,565,428 – 31,785,796 220,368.0 0.00715912 10 112.5039 1,777.7
S_Tubalar-1B + S_Kinh-2A Discordant SGDP 31,176,181 – 31,795,978 619,797.0 0.23319253 42 485.0566 1,731.8
S_Mansi-2B + S_Chechen-1B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Dusun-1B Discordant SGDP 31,575,111 – 31,795,978 220,867.0 0.00751377 10 113.0272 1,769.5
S_Mansi-2B + S_Turkish-2A Discordant SGDP 31,687,839 – 32,277,373 589,533.5 0.43464838 71 631.6948 2,247.9
S_Tubalar-1B + S_Maori-1B Discordant SGDP 31,601,307 – 31,983,119 381,812.0 0.26354286 22 395.1041 1,113.6
S_Tubalar-1B + S_Hungarian-2B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Papuan-3A Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Bergamo-1A Discordant SGDP 31,112,961 – 31,785,796 672,835.0 0.28004278 45 547.9950 1,642.4
S_Tubalar-1B + S_Bougainville-1B Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 8 50.0281 3,198.2
S_Tubalar-1B + S_Sardinian-1B Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 7 50.0281 2,798.4
S_Tubalar-1B + S_Papuan-5B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Jordanian-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Papuan-4A Discordant SGDP 31,565,428 – 31,983,119 417,690.5 0.26588415 20 414.1988 965.7
S_Tubalar-1B + B_Dai-4B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Papuan-14A Discordant SGDP 31,075,226 – 31,983,119 907,892.5 0.57824643 46 899.3855 1,022.9
S_Tubalar-1B + B_Papuan-15A Discordant SGDP 31,785,735 – 32,452,204 666,469.5 0.48873303 66 711.8918 1,854.2
S_Tubalar-1B + S_Papuan-9B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 10 118.3047 1,690.6
S_Tubalar-1B + S_Karitiana-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Papuan-2A Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Tubalar-1B + S_Pima-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Chukchi-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + B_Australian-4A Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 6 50.0281 2,398.7
S_Tubalar-1B + S_Itelman-1A Discordant SGDP 31,112,961 – 31,868,351 755,390.0 0.28655455 45 592.8308 1,518.1
S_Mansi-2B + S_Papuan-3B Discordant SGDP 31,041,075 – 31,868,351 827,276.0 0.37217585 81 695.8332 2,328.1
S_Tubalar-1B + S_Mala-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 157.3398 1,652.5
S_Mansi-2B + S_Papuan-10A Discordant SGDP 31,565,428 – 32,048,924 483,495.5 0.34492814 19 509.0204 746.5
S_Tubalar-1B + S_Mala-3B Discordant SGDP 31,575,111 – 31,795,978 220,867.0 0.00751377 11 113.0272 1,946.4
S_Mansi-2B + S_Papuan-4A Discordant SGDP 31,139,237 – 32,043,090 903,853.5 0.56728663 56 888.6790 1,260.3
S_Tubalar-1B + S_Brahmin-1A Discordant SGDP 31,040,456 – 31,795,978 755,522.0 0.37147296 67 660.8289 2,027.8
S_Mansi-2B + S_Papuan-12A Discordant SGDP 31,565,428 – 32,048,924 483,495.5 0.34492814 18 509.0204 707.2
S_Tubalar-1B + S_Madiga-1B Discordant SGDP 31,575,111 – 31,795,978 220,867.0 0.00751377 13 113.0272 2,300.3
S_Mansi-2B + S_Khonda_Dora-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Madiga-2A Discordant SGDP 31,134,695 – 31,785,796 651,101.0 0.24402329 48 508.7471 1,887.0
S_Mansi-2B + S_Brahui-1B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Pathan-1A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Finnish-1B Discordant SGDP 31,785,735 – 33,231,339 1,445,604.0 0.79522680 197 1,331.0714 2,960.0
S_Tubalar-1B + S_Pathan-2B Discordant SGDP 31,094,427 – 31,785,796 691,369.5 0.29577089 42 569.4741 1,475.0
S_Mansi-2B + S_French-2A Discordant SGDP 31,106,698 – 31,785,796 679,098.5 0.28979702 48 558.8049 1,718.0
S_Tubalar-1B + S_Burusho-2B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Georgian-1B Discordant SGDP 31,697,077 – 31,785,796 88,719.5 0.00206353 7 45.2362 3,094.9
S_Tubalar-1B + S_Abkhasian-1B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Mansi-2B + S_Greek-2B Discordant SGDP 31,565,428 – 32,353,201 787,773.0 0.44553478 41 735.5589 1,114.8
S_Tubalar-1B + S_Bulgarian-1B Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Sardinian-2A Discordant SGDP 31,106,698 – 31,785,796 679,098.5 0.28979702 43 558.8049 1,539.0
S_Tubalar-1B + S_English-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Kyrgyz-2A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 8 138.2450 1,157.4
S_Tubalar-1B + S_Estonian-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Mansi-2B + S_Polish-1A Discordant SGDP 31,601,307 – 31,988,126 386,819.5 0.27456506 20 406.3254 984.4
S_Tubalar-1B + S_Estonian-2B Discordant SGDP 31,134,695 – 31,795,978 661,282.5 0.24516534 45 514.5479 1,749.1
S_Mansi-2B + S_Lezgin-1A Discordant SGDP 31,700,429 – 31,785,796 85,367.5 0.00191709 6 43.5101 2,758.0
S_Tubalar-1B + S_Estonian-1B Discordant SGDP 31,785,735 – 31,795,978 10,243.0 0.00114214 4 6.8304 11,712.4
S_Mansi-2B + S_Spanish-2A Discordant SGDP 31,785,735 – 31,785,796 61.5 0.00000010 4 1.0296 77,700.4
S_Tubalar-1B + S_Finnish-2A Discordant SGDP 31,041,075 – 31,795,978 754,902.5 0.36680613 45 656.7981 1,370.3
S_Mansi-2B + B_Sardinian-3A Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 6 50.0281 2,398.7
S_Tubalar-1B + S_Saami-1A Discordant SGDP 31,687,839 – 31,785,796 97,957.0 0.00251094 7 50.0281 2,798.4
View as figure
Data shown in this table can be downloaded from this page.
α Shape parameter of the Gamma distribution, calculated from the number of pairwise differences along the sequence of the inferred shared haplotype segment (mutation clock), or the breakpoints detected (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
β Rate parameter of the Gamma distribution, calculated from the physical length of the inferred shared haplotype segment and the mutation rate (mutation clock), or the genetic length given the variable recombination rate (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
Mean TMRCA Calculated as the mean of the Gamma distribution with parameters α and β, multiplied by 2 x Ne, where Ne = 10,000 by default.
 

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